I was bemused to find a Linux live disk unable to identify the storage volume on my new Dell XPS 13 laptop. It seemed I needed to change the SATA controller mode from `RAID` to `AHCI`, but Windows had other ideas. Unable to find a solution online that didn’t cause a boot BSOD, I found my own.
I wanted a BAM that contained reads aligned to just one of the many contigs the file contained. As usual, I made this much more difficult than it really ought to have been.
This afternoon I wanted to quickly check whether some reads in a BAM would be filtered out by the GATK `MalformedReadFilter`. Turns out that GATK is pretty unforgiving if you forget that filter is automatically applied by `PrintReads`.
Recently I’ve been following the GATK DNASeq Best Practice Pipeline for my limpet sequence data. Here are some of the mistakes I made and how I made them go away.
I’m still alive, here’s some things what I’ve done.
My datasets are so big, they trigger an NFS bug in the kernel
I purchased a Fitbit Charge HR this morning. Although primarily motivated by my partner’s latest pursuit for improved fitness, I guess any excuse for self-quantification is a good one for a statistician like me.
In my previous post, I admitted to switching back to WordPress. Here is what I learned and some of the pros and cons I’ve encountered so far.
I’d fallen in and out of love with WordPress years ago, but I’ve come full circle, betrayed my vow to never use WordPress again and am trying it out for myself, once more. Here’s why.